Daniela S. Mueller wrote:
[...]
If you have one chain, you don't have to worry about jumps.
In addition, from the cases that I have encountered, you can have
ligands and/or cofactors (non-covalently) bound to an enzyme, and e.g.
counter-ions for which you want to analyze the position in relat
Dear Maxim,
On Mon, 2006-02-27 at 18:14 +, Maxim Fedorov wrote:
> Dear Daniela, dear all.
> Sorry, my previous reply was corrupted
> by our server - as a result it lost any sense.
> You wrote:
> >
> > If the molecule you want to analyse is a single molecule, the
> > jumping of
> > box bound
Maxim Fedorov wrote:
What do you exactly mean when you are saying 'subunits'
A molecule.
--
Groetjes,
Anton
* NOTE: New Affiliation, Phone & Fax numbers (below) *
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Hi Daniela,Are you absolutely sure that in your case the -pbc nojump option CAUSES the rotation? Or could it be that your molecule is rotated a bit, and due to a too large difference between the reference and the starting frame, this causes weird results (I've had that, but that was definitely my m
Hi Maxim,
On Mon, 2006-02-27 at 16:56 +, Maxim Fedorov wrote:
> Dear Daniela,
>
> > If the molecule you want to analyse is a single molecule, the
> > jumping of
> > box boundaries does not matter and the analysis tools take that into
> > account. But if your molecule is a complex of two or
Dear Daniela, dear all.
Sorry, my previous reply was corrupted
by our server - as a result it lost any sense.
You wrote:
>
> If the molecule you want to analyse is a single molecule, the
> jumping of
> box boundaries does not matter and the analysis tools take that into
> account. But if your m
Dear Daniela,
> If the molecule you want to analyse is a single molecule, the
> jumping of
> box boundaries does not matter and the analysis tools take that into
> account. But if your molecule is a complex of two or more separate
> subunits, you might want to remove jumps over the boundaries to
Dear David and Tsjerk,
Thank you very much for your answers -
I'll take care now about the PBC treatment of trajectories.
All the best,
Maxim
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Please do
Hi,Do note how the jumps are removed. First of all, this is done atom-wise. For the first frame, the position of each atom is checked against the position in the given reference, and if there's a distance between them larger than half the box vector, it is shifted back over the lattice. For each su
Daniela S. Mueller wrote:
Dear Maxim, dear David,
On Sun, 2006-02-26 at 22:34 +0100, David van der Spoel wrote:
Maxim Fedorov wrote:
Dear all,
I have been successfully using Gromacs for a couple years without
bothering you -
manual + reading the mailing list was completely enough.
But … t
Dear Maxim, dear David,
On Sun, 2006-02-26 at 22:34 +0100, David van der Spoel wrote:
> Maxim Fedorov wrote:
> > Dear all,
> >
> > I have been successfully using Gromacs for a couple years without
> > bothering you -
> > manual + reading the mailing list was completely enough.
> >
> > But … th
Maxim Fedorov wrote:
Dear all,
I have been successfully using Gromacs for a couple years without
bothering you -
manual + reading the mailing list was completely enough.
But … this is the second mail for this afternoon.
The question is: are there any analysis programs in GROMACS package
whi
Dear all,
I have been successfully using Gromacs for a couple years without
bothering you -
manual + reading the mailing list was completely enough.
But … this is the second mail for this afternoon.
The question is: are there any analysis programs in GROMACS package
which are sensitive to Peri
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